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However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas (PR) and Archean Domes (AD). Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from PR and AD: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and AD: Halanaerobium sp. (63%) and D. halophilus (60%). Furthermore, metagenome-assembled genomes from Ectothiorhodospira genus were found in both AD and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the AD system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin\u2019s biodiversity.<\/jats:p>","DOI":"10.1093\/femsec\/fiaf033","type":"journal-article","created":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T03:23:11Z","timestamp":1744255391000},"source":"Crossref","is-referenced-by-count":4,"title":["Running against the clock: exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert"],"prefix":"10.1093","volume":"101","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4249-0488","authenticated-orcid":false,"given":"Ulises E","family":"Rodriguez-Cruz","sequence":"first","affiliation":[{"name":"Departamento de Ecolog\u00eda Evolutiva, Instituto de Ecolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Ciudad de M\u00e9xico, 04510 ,","place":["M\u00e9xico"]},{"name":"Programa de Doctorado en Ciencias Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Ciudad de M\u00e9xico, 04510 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